Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed

Synonymous but not Silent: The Codon Usage Code for Gene Expression and Protein Folding

(2021) Yi Liu et al.   Annual Review of Biochemistry

Genome-wide role of codon usage on transcription and identification of potential regulators

(2021) Fangzhou Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Domain II of the translation elongation factor eEF1A is required for Gcn2 kinase inhibition

(2020) Rashmi Ramesh et al.   FEBS LETTERS

Circadian clock control of eIF2α phosphorylation is necessary for rhythmic translation initiation

(2020) Shanta Karki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptation of codon usage to tRNA I34 modification controls translation kinetics and proteome landscape

(2020) Xueliang Lyu et al.   PLoS Genetics

Codon Usage and Splicing Jointly Influence mRNA Localization

(2020) Christine Mordstein et al.   Cell Systems

How Does the Ribosome Fold the Proteome?

(2020) Anaïs M.E. Cassaignau et al.   Annual Review of Biochemistry

A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting

(2020) Racha Chouaib et al.   DEVELOPMENTAL CELL

A code within the genetic code: codon usage regulates co-translational protein folding

(2020) Yi Liu   Cell Communication and Signaling

The Ongoing Quest to Crack the Genetic Code for Protein Production

(2020) Thijs Nieuwkoop et al.   MOLECULAR CELL

Nonoptimal Codon Usage Is Critical for Protein Structure and Function of the Master General Amino Acid Control Regulator CPC-1

(2020) Xueliang Lyu et al.   mBio

Puromycin reactivity does not accurately localize translation at the subcellular level

(2020) Syed Usman Enam et al.   eLife

Ribosome quality control antagonizes the activation of the integrated stress response on colliding ribosomes

(2020) Liewei L. Yan et al.   MOLECULAR CELL

Effects of codon usage on gene expression are promoter context dependent

(2020) Qian Yang et al.   NUCLEIC ACIDS RESEARCH

Activation of GCN2 by the ribosomal P-stalk

(2019) Alison J. Inglis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress

(2019) Colin Chih-Chien Wu et al.   MOLECULAR CELL

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data

(2019) Ajeet K. Sharma et al.   PLoS Computational Biology

Translation affects mRNA stability in a codon-dependent manner in human cells

(2019) Qiushuang Wu et al.   eLife

Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity

(2019) Ernest Mordret et al.   MOLECULAR CELL

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

(2019) Andrea Riba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

eIF2α phosphorylation and the regulation of translation

(2019) Erik Boye et al.   CURRENT GENETICS

eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons

(2019) Qian Yang et al.   NUCLEIC ACIDS RESEARCH

Towards a model of GCN2 activation

(2019) Glenn R. Masson   BIOCHEMICAL SOCIETY TRANSACTIONS

The ribosomal P-stalk couples amino acid starvation to GCN2 activation in mammalian cells

(2019) Heather P Harding et al.   eLife

The cell free protein synthesis system from the model filamentous fungus Neurospora crassa

(2018) Cheng Wu et al.   METHODS

The extent of ribosome queuing in budding yeast

(2018) Alon Diament et al.   PLoS Computational Biology

The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

(2018) Khanh Dao Duc et al.   PLoS Genetics

Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

(2018) Zhipeng Zhou et al.   eLife

Mass spectrometry quantitation of proteins from small pools of developing auditory and vestibular cells

(2018) Jocelyn F. Krey et al.   Scientific Data

Regulation of global translation during the cell cycle

(2018) Vilte Stonyte et al.   JOURNAL OF CELL SCIENCE

Codon usage regulates human KRAS expression at both transcriptional and translational levels

(2018) Jingjing Fu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A small single-domain protein folds through the same pathway on and off the ribosome

(2018) Emily J. Guinn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density

(2017) Yuri V. Svitkin et al.   NUCLEIC ACIDS RESEARCH

Ribosome reinitiation can explain length-dependent translation of messenger RNA

(2017) David W. Rogers et al.   PLoS Computational Biology

Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights

(2017) Lucas D. Fernandes et al.   Scientific Reports

The integrated stress response

(2016) Karolina Pakos‐Zebrucka et al.   EMBO REPORTS

Codon usage affects the structure and function of theDrosophilacircadian clock protein PERIOD

(2016) Jingjing Fu et al.   GENES & DEVELOPMENT

Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

(2016) Xavier Pichon et al.   JOURNAL OF CELL BIOLOGY

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

Codon usage is an important determinant of gene expression levels largely through its effects on transcription

(2016) Zhipeng Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

(2016) David E. Weinberg et al.   Cell Reports

Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation

(2016) Ryuta Ishimura et al.   eLife

Roles for Synonymous Codon Usage in Protein Biogenesis

(2015) Julie L. Chaney et al.   Annual Review of Biophysics

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo

(2015) David J. Young et al.   CELL

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding

(2015) Chien-Hung Yu et al.   MOLECULAR CELL

Nonoptimal codon usage influences protein structure in intrinsically disordered regions

(2015) Mian Zhou et al.   MOLECULAR MICROBIOLOGY

Gel-free mass spectrometry analysis ofDrosophila melanogasterheads

(2015) Jana Aradska et al.   PROTEOMICS

Cotranslational protein folding on the ribosome monitored in real time

(2015) W. Holtkamp et al.   SCIENCE

Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast

(2015) Jeffrey A. Hussmann et al.   PLoS Genetics

The Scanning Mechanism of Eukaryotic Translation Initiation

(2014) Alan G. Hinnebusch   Annual Review of Biochemistry

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

(2014) Hila Gingold et al.   CELL

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Ribosome recycling induces optimal translation rate at low ribosomal availability

(2014) E. Marshall et al.   Journal of the Royal Society Interface

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

(2014) C. Pop et al.   Molecular Systems Biology

Phosphorylation of Initiation Factor eIF2 in Response to Stress Conditions Is Mediated by Acidic Ribosomal P1/P2 Proteins in Saccharomyces cerevisiae

(2014) Antonio Jiménez-Díaz et al.   PLoS One

Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates

(2014) Edward P. O’Brien et al.   Nature Communications

The Specification and Global Reprogramming of Histone Epigenetic Marks during Gamete Formation and Early Embryo Development in C. elegans

(2014) Mark Samson et al.   PLoS Genetics

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Translation elongation can control translation initiation on eukaryotic mRNAs

(2013) Dominique Chu et al.   EMBO JOURNAL

Accurate Label-Free Protein Quantitation with High- and Low-Resolution Mass Spectrometers

(2013) Jocelyn F. Krey et al.   JOURNAL OF PROTEOME RESEARCH

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

(2013) Mian Zhou et al.   NATURE

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

(2013) Yao Xu et al.   NATURE

Structural basis for potent inhibitory activity of the antibiotic tigecycline during protein synthesis

(2013) L. Jenner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rare Codons Regulate KRas Oncogenesis

(2012) Benjamin L. Lampson et al.   CURRENT BIOLOGY

New functions of protein kinase Gcn2 in yeast and mammals

(2012) José R. Murguía et al.   IUBMB LIFE

Prediction of variable translation rate effects on cotranslational protein folding

(2012) Edward P. O'Brien et al.   Nature Communications

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Evidence That Eukaryotic Translation Elongation Factor 1A (eEF1A) Binds the Gcn2 Protein C Terminus and Inhibits Gcn2 Activity

(2011) Jyothsna Visweswaraiah et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Dual role of methionyl-tRNA synthetase in the regulation of translation and tumor suppressor activity of aminoacyl-tRNA synthetase-interacting multifunctional protein-3

(2011) N. H. Kwon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evolutionary Roles of Upstream Open Reading Frames in Mediating Gene Regulation in Fungi

(2009) Heather M. Hood et al.   Annual Review of Microbiology

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Experimentally Increased Codon Bias in the Drosophila Adh Gene Leads to an Increase in Larval, But Not Adult, Alcohol Dehydrogenase Activity

(2009) W. Hense et al.   GENETICS

qiRNA is a new type of small interfering RNA induced by DNA damage

(2009) Heng-Chi Lee et al.   NATURE

Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa

(2009) Takao Kasuga et al.   PLoS One

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE